Variant report

Variant	rs3812778
Chromosome Location	chr11:35277270-35277271
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:35275813..35278211-chr11:35282248..35285772,3	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10444271	1.00[YRI][hapmap]
rs10488813	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10836347	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.83[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs10836349	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10836352	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10836353	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10836358	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11033031	1.00[ASW][hapmap];0.93[CEU][hapmap];0.87[GIH][hapmap];0.90[EUR][1000 genomes]
rs11033034	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11033039	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11033041	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11033042	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11033043	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11033071	1.00[YRI][hapmap]
rs12360706	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12364027	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12575005	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1570216	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16927292	0.84[MKK][hapmap];1.00[YRI][hapmap]
rs3794097	0.92[MKK][hapmap];1.00[YRI][hapmap]
rs3829280	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3891872	1.00[YRI][hapmap]
rs4083481	1.00[YRI][hapmap]
rs41525047	1.00[YRI][hapmap]
rs4503504	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4508184	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55715534	0.82[EUR][1000 genomes]
rs56193087	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67384276	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7104662	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7122374	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72638195	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72916162	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045837	chr11:34893992-35395190	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv541004	chr11:35122694-35297414	Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3812778	RAG2	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:35264400-35281800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:35264800-35281800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr11:35265800-35305800	Weak transcription	HepG2	liver
4	chr11:35269400-35281800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr11:35270200-35278200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr11:35270200-35292600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr11:35270400-35277600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr11:35270400-35277600	Weak transcription	Brain Anterior Caudate	brain
9	chr11:35270400-35285400	Weak transcription	Brain Germinal Matrix	brain
10	chr11:35270400-35296400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr11:35270400-35307000	Weak transcription	Fetal Brain Male	brain
12	chr11:35270600-35277600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr11:35270600-35277600	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr11:35270600-35278000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr11:35270600-35278000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr11:35270600-35281000	Weak transcription	Fetal Brain Female	brain
17	chr11:35270600-35284400	Weak transcription	Brain Hippocampus Middle	brain
18	chr11:35271200-35277400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr11:35271200-35286400	Weak transcription	Pancreas	Pancrea
20	chr11:35272600-35278000	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr11:35274600-35287400	Weak transcription	HSMMtube	muscle
22	chr11:35275000-35281800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr11:35275400-35281800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:35275600-35277400	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr11:35275800-35281000	Weak transcription	NHDF-Ad	bronchial
26	chr11:35275800-35281200	Weak transcription	NHLF	lung
27	chr11:35275800-35281400	Weak transcription	Colon Smooth Muscle	Colon
28	chr11:35276000-35281000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr11:35276200-35277800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr11:35276400-35277800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr11:35277000-35278600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr11:35277000-35278600	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr11:35277000-35279000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr11:35277000-35282000	Weak transcription	Aorta	Aorta
35	chr11:35277200-35282000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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